Young Justice:Not alone
by Shadowed sword
Summary: What if the DC world wasn't just a hot spot for aliens? what if one hero was added in and there was more to him than even he knows? Join Danny and the team as they fight new and old foes and more importantly unravel the mysteries surrounding Danny's true past
1. Chapter 1

**A/N: Hey I am back and I got this great idea and I hope everyone likes it I own nothing except the plot and some of the history**

He had to get away they were gaining and he couldn't let them get him it would be horrible for everyone if he was. He could see them he was almost free when suddenly..."AHHHHHHHHHHH" Danny Phantom screamed awakening from a dream or maybe nightmare he couldn't tell anymore they were all the same now. He looked around and still saw the same blank white walls of his cell in Cadmus. He hated It here and wanted to escape but the scars on his chest were a reminder that Cadmus didn't like that he looked in the mirror and it still got him how much had changed since the day he had got captured. Before he was captured he was about 5'5 and pretty skinny but had muscle and had minimal powers from his ghost side compared to some of his foes, but the day he had been captured was also the day he finally woke up from a sleep while his ghost body went through a power up for the ghost it was different than normal because of how powerful Danny was. Normally ghost wouldn't go through this sleep until they were a few centuries old, by that time they had reached the necessary power requirement that being a class 3 or class 4 but Danny who started out at class 1 had shot through them and ever since he fought Nocturne he had been teetering on a class 5 a class only Pariah and Overgrowth had been in but needed a push that came when Overgrowth attacked. Whenever Danny had beat a ghost a small amount of power slipped from them and went to him why that happened is because, when ghosts fight the winner of the fight that is given power that why ghosts fight so much but when a weaker class defeats a stronger class more power is given to the loser but they must hold onto it for a month and not be defeated by the ghost they won it from for it to be theirs except if they go through a major class change.

The classes are this: Class 1-sentient has obsession and has some form and 1 or 2 powers, Class 2-has human like form mostly and has at least 2 or 3 powers and some personality, Class 3-human like has 3 or more powers and is generally smarter than others, Class 4- human like or monstrous has 3 or more powers has a Domain and is considered to be a god or more in human world, Finally Class 5-human like with unearthly feature has lots of powers and blessed by Lady Death herself is considered to be primordial or a literal force of nature. When Danny had ascended he had learned why he survived the portal. Lady Death had wanted a child and when the portal accident happened she had acted and made Danny's ghost side her son by doing that she had gained a more human like appearance and a power upgrade but when he ascended it killed his human half because no human body could handle the amount of power he had. He now looked 6'0 and his hair was now white with neon blue streaks and his eyes were now glowing ice blue with neon green iris he had muscle and he now wore a blue t-shirt and black pants and he also wore a blue and black tattered Cape with a hood.

Danny had grown accustomed to his ghost form and had learned of a few things while at Cadmus he learned how to control his powers to perfection he also found that his blessing was unparalleled control of Ice and the elements that made it up. He also found out that his strength was at least equal to SuperMan's as he had heard some scientists that they might not need project Kr because of him. The last thing he had learned was that there was another project that was going to be attempted but he hadn't learned what or who it was. He snapped out of his reprieve when he heard some sounds like there was a fire going on up above. He was just about to ask a scientist that was outside of the cell he was in what was going on when the scientist pressed a button and the next thing he knew he was waking up in another cell this one more heavily enforced.

He was extremely agitated he had heard some people enter and had heard them pass down the opposite hall when he heard them again coming back he immediately knew he could get out of here if he was loud enough so he gathered air and shouted "HEY GET ME OUT OF HERE" he heard the people stop before they rushed over (Everyone knows what they look like if you don't look up young justice) Robin immediately started typing and he said to his team "Project Primordial the subject is one of the only known Primordial Class entities in existence and is probably the most powerful when conditioned will be used to wipe out at least half of the League if growth stays the same". The team and Superboy were in shock that Cadmus thought this man could take out half the League Robin quickly tried to disable the shields but was only able to weaken them when he was about to say that to the man he simply placed a hand on the shield when he felt it weaken and it shattered. Before they could ask he told them to follow him and led them to the top floor where they encountered Desmond just as he was about to drink the blockbuster formula he was frozen by a beam from the man who introduced himself as Phantom.

After they got outside they were surrounded by the League they explained everything but before they could explain about Phantom they saw him looking around before his head snapped to one direction and shouted

 **A/N:I am loving this and I am going to put up a new poll about who Danny should be with a Ghost a Hero or a Villain vote for which ones review votes count as well**


	2. Chapter 2

**A/N: Hey I am back with another chapter and I am shocked I could not believe it how many people like this story and for all that do check out my other one's and for my pokemon fans out there I am working on the second chapter of Dark Betrayal I finally found the story that gave me my muse for it vote on the poll just so you know Danny will be Darker because of what Cadmus did and thank you RedBurningDragon for your idea I will be using it because I can see it and it works for the story so without further ado please enjoy**

"DANIELLE!" Was shouted by Phantom as he took off at speeds that SuperMan and Flash were hard pressed to match. As soon as Phantom took off the League and the Sidekicks went after him they didn't have to go far as they all saw him floating above a group of 5 Villains. The League was about to jump in but they saw something that made them stop thrown to the ground in the middle of the group of Villains was a female looking Phantom and her clothes were in tatters. Batman's eyes flew wide open as he calculated what was going on and he knew without any doubt that the girl down there was Phantom's daughter and taking that into account he turned to try to stop him but he was too slow this one time. With a roar of absolute fury Phantom shot from his position and threw one of the group into another with two down Phantom shot a beam of ice at the other two and turned to the last one the only female in the group of males. Just as he was about to move Danielle who was watching and had pieced together who it was stood in front of Poison Ivy and said "Daddy please stop she protected me from the things they were going to do to me" Phantom looked at her then looked at Ivy who nodded after that he made a get lost gesture which she took and ran off.

Some of the League were about to go after her when Batman said to leave it and they needed to get the four that were knocked out back to prison and talk to Phantom who was busy consoling his daughter and explaining everything to her. After they had taken the knocked out Villains to prison they all went to mount justice where they sat around a table at least most of them Phantom and Danielle choose to hover."So what do you want to know" Phantom said normally he would have just left but after they had saved him and had basically allowed him to save his daughter he was willing to part with information."What and Who are you we want to know" Batman said in a surprisingly less commanding voice than he usually used. "This is gonna take awhile" Phantom said as he started to explain who he was when he was alive and what he had went through. He told them of his accident his time fighting ghosts which he proved to them by doing things no human or alien could do, he explained what he remembered of his fight with a Fallen Primordial called Pariah Dark, he explained his meeting the master of time and working under him for a year and the adventures he had then, he then told them all he could remember of his fight with his alternate self, finally he told them of his fight with another Primordial called Undergrowth and his own awakening into becoming the third Primordial and the death of his human half and his time at Cadmus. Some of the members had left after hearing some parts and Danielle and the Young justice team was sent out before he told them of his time at Cadmus.

Batman was shocked and disgusted by what Cadmus had done Phantom had near instantaneous healing and yet he had scars because of what Cadmus had done to him not to mention Cadmus had taken away every last bit of innocence he had left in him. The remaining League members had then called everyone back in and they asked them if they minded making Phantom and Danielle into members of the respective Teams. After the vote with it being a majority for but some against they were allowed to join if they wanted Danielle accepted immediately but Phantom asked for some time to think about it and he was given 1 day to think about it after that everyone went to sleep. During Phantom's sleep he kept getting flashes of stuff that he couldn't see properly but the last few flashes he saw clear as day. In One he was with two grown men in weird suits fighting against a bipedal cat of all things and his hair was glowing green. In the second he saw his fight against Pariah but him saying something about it coming full circle. In the third he saw what he thought was his future him in a tux on an alter and looking at this beautiful women but he couldn't see what she looked like. In the fourth and final flash he saw his fight with Dan but it was different Dan was kneeling and why was he calling him Master.

Phantom jolted awake and shook his head and decided to look into that later right now he needed to decide what he was going to say to everyone. Everyone was back at mount justice and everyone turned to him and he saw a bunch of expressions on everyone's faces and then Batman stepped forward and said "Well what is your decision". Phantom looked down and then said

 **A/N: My first cliffhanger sorry but until the poll is done I can't go further I want at least 20 votes because I plan on introducing his love interest next chapter though depending on what you choose their might be another poll because for 2 options I am stuck between two girls for him now to anyone out there if you have ideas feel free to give them because I may use them I am not saying I will use all of them I am just saying every little bit of help counts for me**


	3. Chapter 3

**A/N: Hello Phans and welcome back and because of all the votes in the reviews and on the polls Danny will be paired with a...Hero it only won by one vote but if you guys want I will add another girl but she will be either a villain or ghost and without further ado let us get back into Young Justice; Not Alone oh and Danny is called Phantom for a different reason than you think or if you think you know put it in a review and I will PM you if you are right I own nothing except the plot**

"Not right now" Was how Phantom answered the question everyone was shocked but Batman looked at him and asked why"I am not fully recovered from my time at Cadmus and I still have to go through another sleep soon" when everyone heard that they asked why and he said that because he was so young when he went through the sleep he didn't gather enough Cosmic Energy. Batman immediately asked him to explain since he had seen what it could do and Phantom explained that each Primordial needed a certain amount and the lower the age the higher amount needed because they could still gather extra and to prevent that and destroying the universe they gathered it in their sleep and it went where it needed to go. He also told them that since he was in danger his body woke up early and he accidentally gathered about as much as another primordial needed since he was in an area rich in Cosmic Energy and the only reason he didn't blow up is that he directed some of the extra to his speed and strength to where it grew in extreme amount. Phantom then said that while at Cadmus it started to regulate itself but when he was broken out he uncontisally gathered up a bit more when he sensed Danielle was in danger which he said was common for Fully realized Primordials and that was why he needed another rest because if he didn't then the energy couldn't direct itself and he would basically have to exile himself to keep everyone safe.

When everyone heard that they were shocked of course some did not believe him so he let them run some tests on him and they found out he was right they also found he was stronger than SuperMan but only by a small amount and that he was faster than almost anyone running except The Flash and Kid Flash but flying he was close to Mach 3 if he pushed it. After that it was decided that Phantom would be up on the Watchtower when he was asleep so no one could grab him at that vulnerable time when asked how long he said anywhere between 2-4 weeks he would just fall asleep. So after he was taken to the Watchtower he was left with almost completely free roam of the place but he had to have someone watch him after a vote and a discussion they decided that the one who would guard him is SuperGirl. So that is how for about a month that Phantom and SuperGirl had nothing to do but hangout chat and generally just talked to one another they found out they had a few things in common with each other and liked some of the same music it came as a surprise that SuperGirl was a fan of Skillet and Five Finger Death Punch. The next day when she went to wake up Phantom who she found out was not an early riser she found him encased in a golden energy that covered him completely she went to the nearest communication device and told Batman since he had kept his clear expecting this and he immediately came up and ran some tests and declared that he would be fine but he didn't know how long he would be asleep so he decided that he would be kept there until he woke up.

2 months that is how long Phantom was sleeping during that time Young Justice was kept in the loop and was told of his progress and told when he was showing signs of waking up they weren't allowed on the Watchtower but they did get a video link so they could see him. When everyone entered the room where he was held they saw that he had changed again he was still the same height but his hair had turned from pure white to half white half icey-blue and he now wore a black t-shirt with a silver skull black jeans and to complete it a tattered cloak that was three colors one part was blue as the sea one part was greenish white and the last part was icey blue but for some strange reason the hood was black(Can someone make a picture and send it to me please). When he awoke everyone saw his eyes had stayed the same and that he was completely refreshed and seemingly at peace with himself when everyone was done asking inane questions Batman asked what he was going to do know and Phantom said he would like to join the League since he had nothing else to even consider right now after staring at him for awhile they accepted him. When Flash asked what his nickname was gonna be for outside the Watchtower he was just given a blank look and after realizing what he said he just awkwardly rubbed his head and laughed after that Phantom was told as he was a new member he had to shadow a hero so they could show him the ropes so to speak before anyone else could speak SuperMan and SuperGirl said that he could shadow them. That brought on an argument with SuperMan basically being overprotective and SuperGirl saying she could take care of herself and it just escalating until Phantom decided to stop it gathering up a small portion of power he flared it and said "Enough" and everyone immediately fell silent after that he took the 2 and dragged them to another place and said some things in a hushed voice to them both at some points it looked like they were gonna argue but he cut it down with a few words.

After they got back to the rest of the group SuperMan agreed to letting his cousin teach Phantom how they did things but before they could disperse they heard some chatter and yelling and they turned to the live screen and they heard was that something was happening in Amity Park when they asked what it was they were told they might need full League support. When they got there they could hardly believe what they saw.

 **A/N: so I am done if you don't like who Danny is with then tough I have my reasons more than one and also Danny is gonna be powerful he is not gonna be perfect but he will take on most opponents that the League and SuperMan struggle with and will take them on with little difficulty but there is a reason and he will have opponents that will beat him it is just being Death's child means his strength is unreal but he can be beaten but he will not be doing that for some time**


End file.
